HACSim: Iterative Extrapolation of Species' Haplotype AccumulationCurves for Genetic Diversity Assessment
Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi:10.7717/peerj-cs.243>. 'HACSim' outputs a number of useful summary statistics of sampling coverage ("Measures of Sampling Closeness"), including an estimate of the likely required sample size (along with desired level confidence intervals) necessary to recover a given number/proportion of observed unique species' haplotypes. Any genomic marker can be targeted to assess likely required specimen sample sizes for genetic diversity assessment. The method is particularly well-suited to assess sampling sufficiency for DNA barcoding initiatives. Users can also simulate their own DNA sequences according to various models of nucleotide substitution. A Shiny app is also available.
| Version: | 1.0.7-1 |
| Imports: | ape (≥ 5.3),data.table (≥ 1.12.8), graphics (≥ 3.6.1),matrixStats (≥ 0.56.0),pegas (≥ 0.13),Rcpp (≥ 1.0.3), stats (≥ 3.6.1),stringr (≥ 1.5.0), utils (≥ 3.6.1) |
| LinkingTo: | Rcpp,RcppArmadillo |
| Published: | 2025-09-19 |
| DOI: | 10.32614/CRAN.package.HACSim |
| Author: | Jarrett D. Phillips [aut, cre], Steven H. French [ctb], Navdeep Singh [ctb] |
| Maintainer: | Jarrett D. Phillips <phillipsjarrett1 at gmail.com> |
| License: | GPL-3 |
| URL: | <https://github.com/jphill01/HACSim.R><https://github.com/jphill01/HACSim-RShiny-App><https://jphill01.shinyapps.io/HACSim> |
| NeedsCompilation: | yes |
| CRAN checks: | HACSim results |
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